library(dplyr)
library(magrittr)
load(params$RData_image)
plot_precentage_of_samples_over_min_abd
Figure 1: Percentage of coverage
plot_precentage_of_samples_over_min_abd_byRun
Figure 2: Percentage of coverage per Run
plot_precentage_of_samples_over_min_abd_byVariable1
Figure 3: Percentage of coverage per catagories in Variable1
print(paste0(length(n_off_target_alleles), ' allele(s) match(es) the criteria to define off-target products'))
## [1] "0 allele(s) match(es) the criteria to define off-target products"
print(paste0(length(n_flanking_INDEL_alleles), ' allele(s) match(es) the criteria to identify products with flanking INDELs'))
## [1] "0 allele(s) match(es) the criteria to identify products with flanking INDELs"
print(paste0(length(n_PCR_errors_alleles), ' allele(s) match(es) the criteria to identify PCR_errors'))
## [1] "13 allele(s) match(es) the criteria to identify PCR_errors"
if(length(n_off_target_alleles) > 0){
plot_off_target_stats
}
if(length(n_off_target_alleles) > 0){
off_target_stats%>%
DT::datatable(extensions = 'Buttons',
options = list(dom = 'Blfrtip',
buttons = c('csv', 'excel')))
}
if(length(n_flanking_INDEL_alleles) > 0){
plot_flanking_INDEL_stats
}
if(length(n_flanking_INDEL_alleles) > 0){
flanking_INDEL_stats%>%
DT::datatable(extensions = 'Buttons',
options = list(dom = 'Blfrtip',
buttons = c('csv', 'excel')))
}
if(length(n_PCR_errors_alleles) > 0){
plot_PCR_errors_stats
}
Figure 5: Flanking INDELs
if(length(n_PCR_errors_alleles) > 0){
PCR_errors_stats%>%
DT::datatable(extensions = 'Buttons',
options = list(dom = 'Blfrtip',
buttons = c('csv', 'excel')))
}
ReadDepth_coverage$plot_read_depth_heatmap
Figure 5: Read Coverage per sample per locus
ReadDepth_coverage_by_run$plot_read_depth_heatmap
Figure 5: Read Coverage per sample per locus by run
ReadDepth_coverage_by_run_controls$plot_read_depth_heatmap
Figure 5: Read Coverage of controls per locus by run
all_loci_amplification_rate
Figure 5: Locus amplification rate distribution
samples_amplification_rate
Figure 5: Sample amplification rate distribution
Cigar table without masking and filter
cigar_table_unmasked_unfiltered %>%
DT::datatable(extensions = 'Buttons',
options = list(dom = 'Blfrtip',
buttons = c('csv', 'excel')))
Masked and filtered cigar table without controls
cigar_table_masked_filtered %>%
DT::datatable(extensions = 'Buttons',
options = list(dom = 'Blfrtip',
buttons = c('csv', 'excel')))
Masked and filtered cigar table of controls
cigar_table_controls_masked_filtered %>%
DT::datatable(extensions = 'Buttons',
options = list(
buttons = c('csv', 'excel')))